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Sword TT, Dinglasan JLN, Abbas GS, William Barker J, Spradley ME, Greene ER, Gooden DS, Emrich SJ, Gilchrist MA, Doktycz MJ, Bailey CB. Profiling Expression Strategies for a Type III Polyketide Synthase in a Lysate-Based, Cell-free System. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569483. [PMID: 38077034 PMCID: PMC10705458 DOI: 10.1101/2023.11.30.569483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Some of the most metabolically diverse species of bacteria (e.g., Actinobacteria) have higher GC content in their DNA, differ substantially in codon usage, and have distinct protein folding environments compared to tractable expression hosts like Escherichia coli. Consequentially, expressing biosynthetic gene clusters (BGCs) from these bacteria in E. coli frequently results in a myriad of unpredictable issues with protein expression and folding, delaying the biochemical characterization of new natural products. Current strategies to achieve soluble, active expression of these enzymes in tractable hosts, such as BGC refactoring, can be a lengthy trial-and-error process. Cell-free expression (CFE) has emerged as 1) a valuable expression platform for enzymes that are challenging to synthesize in vivo, and as 2) a testbed for rapid prototyping that can improve cellular expression. Here, we use a type III polyketide synthase from Streptomyces griseus, RppA, which catalyzes the formation of the red pigment flaviolin, as a reporter to investigate BGC refactoring techniques. We synergistically tune promoter and codon usage to improve flaviolin production from cell-free expressed RppA. We then assess the utility of cell-free systems for prototyping these refactoring tactics prior to their implementation in cells. Overall, codon harmonization improves natural product synthesis more than traditional codon optimization across cell-free and cellular environments. Refactoring promoters and/or coding sequences via CFE can be a valuable strategy to rapidly screen for catalytically functional production of enzymes from BCGs. By showing the coordinators between CFE versus in vivo expression, this work advances CFE as a tool for natural product research.
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Affiliation(s)
- Tien T. Sword
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Jaime Lorenzo N. Dinglasan
- Biosciences Division, Oak Ridge National Laboratory (Oak Ridge, TN USA)
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
| | - Ghaeath S.K. Abbas
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
- University of Sydney, School of Chemistry (Sydney, NSW, Australia)
| | - J. William Barker
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Madeline E. Spradley
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Elijah R. Greene
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Damian S. Gooden
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Scott J. Emrich
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
- Department of Electrical Engineering and Computer Science, University of Tennessee-Knoxville (Knoxville, TN USA)
- Department of Ecology & Evolutionary Biology, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Michael A. Gilchrist
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
- Department of Ecology & Evolutionary Biology, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory (Oak Ridge, TN USA)
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
| | - Constance B. Bailey
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
- University of Sydney, School of Chemistry (Sydney, NSW, Australia)
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